[gmx-users] Re: PME slows down

[David van der Spoel]

> >
> > Hard to say, check energy and density anyway.
> Energy and density are normal.
> > Which gromacs version? Is the machine out of memory?
> v3.2, memory is fine.
> > Are there other jobs running (run top).
> nope.
> > > >
> > > > >        /Jason
> > > > --
> > > > David.
> > > >
> 
> As I mentioned before, the only abnormality I can see are the constraint
> warnings in the log file. Could it be that mdrun is spending more and more
> time in constraint iteration loops?
> 
No, it is not iterative.

Try breaking the jobs in pieces of a few ns. Did you use shuffling or
sorting?
>  /Jason
> 
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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